Dan Vasilescu

Unary operator precedence ignored by ASTNode parser.

6

Given this expression (konm * (h ^ - 1.0) / koffm), parsing it with the ASTNode parser will result in an error for the unary operator. The following equivalent expression...

ClassCastException in SBMLReader

1

The attached xml file triggers the following exception: java.lang.ClassCastException: class org.sbml.jsbml.xml.XMLNode cannot be cast to class org.sbml.jsbml.Annotation (org.sbml.jsbml.xml.XMLNode and org.sbml.jsbml.Annotation are in unnamed module of loader 'app') at org.sbml.jsbml.xml.stax.SBMLReader.readXMLFromXMLEventReader(SBMLReader.java:851) The...

Postprocessing in the Langevin solver

2

1. Postprocessing current job data 2. Separate instance of the solver that will be invoked by slurm after the parallel jobs are finished 3. implement the postprocessing algorithm (averages, std,...

Langevin Solver code maintenance

9

Solver code maintenance 1. Fix bugs in the solver 2. modify the code to implement new algorithms (lambda, on / off rate 3. add sanity checks in the client

Running Langevin Solver in parallel using slurm

1

Running Langevin Solver in parallel using slurm 1. proof of concept, n jobs, m processors 2. implement test to launch fake jobs 3. test to launch langevin

new panel (table) for cluster analysis results display ACS, ACO, SD for mean run, overall run, individual runs (maybe, could be too much junk if hundreds of runs)

Graphically display averages, standard deviation, min and max for observables over multiple runs

Automate the code in PR #1496 - branch dan-bmdb-unsupported to: run the SBML import against all BMDB models periodically (e.g. every week) and make a discrepancy report to send to...